Sorry if it is a stupid question, but I can't figure out how to do this...
I downloaded commons-net-3.1 from commons.apache.org and I don't know how to have it in my Java System Library or anywhere else I can use it from. I need to use org.apache.commons.io.FileUtils.
This might be overkill for what you're trying to do, but please use a dependency management system instead of managing your dependencies manually. It's a bit more setup now, but you'll reap the rewards later (and anyone else working on your project will thank you).
Take a look at maven, for example.